Abstract
BackgroundHigh-resolution cytogenetic map can provide not only important biological information on genome organization but also solid foundation for genetic and genomic research. The progress in the molecular and cytogenetic studies has created the basis for developing the cytogenetic map in cucumber (Cucumis sativus L.).ResultsHere, the cytogenetic maps of four cucumber chromosomes (chromosomes 1, 3–5) were constructed by fluorescence in situ hybridization (FISH) analysis on cucumber pachytene chromosomes. Together with our previously constructed cytogenetic maps of three cucumber chromosomes (chromosomes 2, 6–7), cucumber has a complete cytogenetic map with 76 anchoring points between the genetic, the cytogenetic and the draft genome assembly maps. To compare our pachytene FISH map directly to the genetic linkage and draft genome assembly maps, we used a standardized map unit—relative map position (RMP) to produce the comparative map alignments. The alignments allowed a global view of the relationship of genetic and physical distances along each cucumber chromosome, and accuracy and coverage of the draft genome assembly map.ConclusionsWe demonstrated a good correlation between positions of the markers in the linkage and physical maps, and essentially complete coverage of chromosome arms by the draft genome assembly. Our study not only provides essential information for the improvement of sequence assembly but also offers molecular tools for cucumber genomics research, comparative genomics and evolutionary study.
Highlights
High-resolution cytogenetic map can provide important biological information on genome organization and solid foundation for genetic and genomic research
The construction of molecular cytogenetic maps of cucumber chromosomes 1, 3–5 To construct the molecular cytogenetic maps of the remaining four cucumber chromosomes, we selected a set of fosmid clones distributed at regular intervals across the chromosome-level cucumber draft genome assembly maps
We first determined the physical order of adjacent fosmid clones based on their positions in draft genome assembly map by dual-color fluorescence in situ hybridization (FISH) on somatic metaphase chromosomes (Figures 1a1-a4)
Summary
High-resolution cytogenetic map can provide important biological information on genome organization and solid foundation for genetic and genomic research. Cucumber (Cucumis sativus L., 2n = 2x = 14), which belongs to the family Cucurbitaceae, is an economically important crop as well as a model system to study biologically relevant characters such as sex determination [1] and plant vascular biology [2] For these reasons, sequencing of the cucumber genome and the development of functional genomic tools are of great importance. Genetic linkage map is usually good indicator of the marker order, the exact physical positions of the genetic loci and genomic sequences on the chromosomes are unknown This is because crossovers are not distributed over chromosome arms, and as a result loci that are physically far apart on chromosomes can be tightly linked on linkage maps and vice versa. Such discrepancies are impediments to applying linkage maps to guide genome sequence assembly
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
